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1. What is the batch computing limit?

   In order to make sure that the system works properly, and to avoid system suspended animation or session-timeout, we set a limit of the number of molecules uploaded for each calculator. The default is 5000. If there are some very large molecules, please reduce the number in response to the situation.

2. What are the format requirements for the input files in the BioChem, BioProt and BioDNA?

   Format requirement

   Calculator	Supported input file format
   BioChem	*.smi, *.sdf
   BioProt	*.fasta
   BioDNA	*.fasta

3. What are the format requirements for the input files in BioCCI, BioPPI and BioDDI?

   Here are two example files for each step. Users should prepare the input file like this:

   Example file for step 1

   c1	C(C=CC1)=C(C=1)CO
   c2	C(C(=CC1)C=C)=C(C=1)CO
   c3	C(C(=CC1)C=C)(=C(C=1)CO)O
   ...	...
   cn	C(NCC1)(CO1)CO

   Example file for step 2

   c1	c2
   c2	c4
   c2	c3
   ...	...
   ck(0 < k < n)	cj(0< j < n)

4. What are the format requirements for the input files in BioCPI, BioDPI and BioCDI?

   Here are three example files for each step. Users should prepare the input file like this:

   Example file for step 1

   c1	C(C=CC1)=C(C=1)CO
   c2	C(C(=CC1)C=C)=C(C=1)CO
   c3	C(C(=CC1)C=C)(=C(C=1)CO)O
   ...	...
   cn	C(NCC1)(CO1)CO

   Example file for step 2

   p1	CANDSDTLELPDSSRALLLGWVPTRLVPALYGLLLLAAVSLDRYLALVHPL
   p2	TLSNFLLSVLVLPFVVTSSIRREWIFGVVWCNFSALLYLLISSASML
   p3	YRTRKLHTPANYLIASLAVTDLLVSILVMPISTMYTVTGRWTLGQVVCDFWL
   ...	...
   pm	TGFCAACHGCLFIACFVLVLTQSSIFSLLAIAIDRYIAIRIPLRYNGLVTGTRAKGIIAICW

   Example file for step 3

   c1	p2
   c2	p4
   c2	p3
   ...	...
   ck(0 < k < n)	pj(0< j < m)

5. What is the calculation step for the interaction features?

   The calculation process for BioCCI, BioPPI and BioDDI is similar to each other.
   Step 1: The molecular structures or sequences of the associated chemicals, proteins, and DNAs/RNAs in the chemical-chemical, protein-protein, and DNA/RNA-DNA/RNA interaction networks are provided to calculate the corresponding molecular features.
   Step 2: The adjacency list file and the molecular features in Step 1 are provided to calculate the final interaction features.
   
   The calculation process for BioCDI, BioCPI and BioDPI is similar to each other.
   Step 1: The molecular structures or sequences of the associated chemicals, proteins, and DNAs/RNAs in the chemical-chemical, protein-protein, and DNA/RNA-DNA/RNA interaction networks are provided to calculate the corresponding molecular features.
   Step 2: The molecular structures or sequences of another molecular object from interaction data are provided to calculate the corresponding molecular features.
   Step 3: The adjacency list file and the molecular features in Step 1 and 2 are provided to calculate the final interaction features. For detailed description, please refer to the documentation section.

6. How are the names of the calculated features defined?

   For BioTriangle, the molecular features or interaction features calculated by different tools have their corresponding names. For BioChem, BioProt and BioDNA, the feature names have very visualized meaning that any people could understand. For BioCCI, BioDDI, BioPPI, BioCPI, BioCDI, and BioDPI, the interaction feature names are defined by two feature names of two molecular objects in the interaction sample.

7. How many features could be calculated by the third way in the process of interaction feature calculation?

   The third way is generated by the outer product of two feature vectors from those chemicals, proteins, and DNAs/RNAs. The number of generated features by the third way may be very tremendous, so the users should apply it according to their needs.

8. How to avoid the 502, 504 Bad Gateway error ?

   In order to make sure that the system works properly, we have a batch computing limit. If you encounter this exception, you should reduce the number of molecules submitted or reduce the features selected.

9. How to avoid the 500 error or Page unavailable?

   In most cases, these errors are probably caused by the wrong input content. Some molecules with wrong structure information can not be handled correctly by the system. Firstly, you should check your molecular files or the SMILES you upload or submit. For the small molecules, we suggest you using the Canonical SMILES instead of unchecked SMILES. Then, you should check the blank lines in your file, especially at the end of the file. Because, incorrect blank lines will lead to I/O errors.

10. Why does the error message pop up when use the correct '*sdf' file?

    It is related with the *.sdf file format.The M CHG and M RAD lines are used for connection tables that ‘overflow’ the allowed atom block limits. By now the M CHG and M RAD lines can not be handled correctly in some cases.